Because of its fundamental role in molecular biological processes, DNA represents an important target for drug action. Compounds that can recognize defined sequences of DNA have a wide variety of potential uses, such as the modulation of gene expression.
The outer surface of double-helical DNA has two channels, namely the major and minor grooves. Both of these grooves contain chemical information by way of arrangements of hydrogen-bond donors and acceptors, electrostatic charges, dipoles, hydrophobic regions and so on.
The major groove contains approximately twice the information content of the minor groove in terms of the number of potential hydrogen-bonding contacts. In view of this, the major groove is the preferred recognition site for cellular proteins such as control proteins, promoters and repressors.
In contrast, the minor groove is normally (with a few exceptions) relatively unoccupied. The vulnerability of the minor groove makes it a particularly useful target for compounds that bind to DNA. Indeed, perhaps for this very reason, the minor groove is the binding site for certain naturally occurring antibiotics (such as netropsin and distamycin).
Netropsin and distamycin are oligopeptides based on pyrrole amino acid monomers. These compounds both bind to DNA with dissociation constants in the order of 10−5 M. They also show a preference for AT-rich regions of DNA. Although they have intrinsic biological activity, netropsin and distamycin also have many limitations including toxicity, moderate affinity and limited selectivity. A number of workers have therefore prepared synthetic analogues of netropsin and distamycin, with a view to overcoming these disadvantages. Many of these compounds are reviewed by Sondhi et al. (Curr. Med. Chem. 4, 313 (1997)), Reddy et al. (Pharmacology & Therapeutics 84, 1 (1999)), Wemmer (Biopolymers 52, 197 (2001)) and Dervan (Bioorg. Med. Chem. 9, 2215 (2001)).
Compounds designed to bind to DNA regions containing GC base pairs are described in, for example: Anti-Cancer Drug Design 5, 3 (1990); Proc. Natl. Acad. Sci. USA 89, 7586 (1992); Biochemistry 32, 4237 (1993); Science 266, 647 (1994); Anti-Cancer Drug Design 10, 155 (1995); Bioorg. Med. Chem. 8, 985 (2000); and Mol. Biol. 34, 357 (2000). Various other netropsin and distamycin analogues are described in: J. Am. Chem. Soc. 114(15), 5911 (1992); Biochemistry 31, 8349 (1992); Bioconjugate Chem. 5, 475 (1994); Biochem. Biophys. Res. Commun. 222, 764 (1996); J. Med. Chem. 43, 3257 (2000); and Tetrahedron 56, 5225 (2000). Further, the use of certain netropsin and distamycin analogues as antimicrobial, antiviral and/or antitumor agents is described in Molecular Pharmacology 54, 280 (1998), Bioorg. Med. Chem. Lett. 6(18), 2169 (1996), J. Med. Chem. 45, 805 (2002), Bioorg. Med. Chem. Lett. 12, 2007 (2002), international patent applications WO 97/28123, WO 98/21202, WO 01/74898 and WO 02/00650, as well as in U.S. Pat. Nos. 4,912,199, 5,273,991, 5,637,621, 5,698,674 and 5,753,629. Methods of synthesizing analogues of netropsin and distamycin are described in U.S. Pat. No. 6,090,947.
Cellular uptake of distamycin analogues is described in Bioorg. Med. Chem. Lett. 11, 769 (2001).
None of the above-mentioned documents describe oligopeptide analogues of netropsin or distamycin, which analogues comprise at least two heterocyclic monomers, at least one of which is substituted in the heterocyclic part by a branched, cyclic or part cyclic C3-5 alkyl group. Surprisingly, we have found that compounds of this type bind with a high affinity and specificity to the minor groove of DNA.